From 55344810a74c559c65d9203324b41a62a99517e3 Mon Sep 17 00:00:00 2001 From: cmzmasek Date: Fri, 1 Nov 2013 20:30:11 +0000 Subject: [PATCH] in progress --- .../src/org/forester/archaeopteryx/TaxonomyUtil.java | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/forester/java/src/org/forester/archaeopteryx/TaxonomyUtil.java b/forester/java/src/org/forester/archaeopteryx/TaxonomyUtil.java index d136c9d..899dfa4 100644 --- a/forester/java/src/org/forester/archaeopteryx/TaxonomyUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/TaxonomyUtil.java @@ -14,6 +14,8 @@ final class TaxonomyUtil { private final static Map _default_taxcode_taxgroup_map = new HashMap(); static { _default_taxcode_taxgroup_map.put( "HUMAN", "deuterostomia" ); + _default_taxcode_taxgroup_map.put( "HOMSA", "deuterostomia" ); + _default_taxcode_taxgroup_map.put( "PANTR", "deuterostomia" ); _default_taxcode_taxgroup_map.put( "GORGO", "deuterostomia" ); _default_taxcode_taxgroup_map.put( "PONAB", "deuterostomia" ); @@ -143,14 +145,22 @@ final class TaxonomyUtil { _default_taxcode_taxgroup_map.put( "ACRDI", "cnidaria" ); _default_taxcode_taxgroup_map.put( "NEMVE", "cnidaria" ); _default_taxcode_taxgroup_map.put( "HMAXX", "cnidaria" ); + _default_taxcode_taxgroup_map.put( "HYDMA", "cnidaria" ); //TODO + _default_taxcode_taxgroup_map.put( "TRIAD", "placozoa" ); _default_taxcode_taxgroup_map.put( "MNELE", "ctenophora" ); _default_taxcode_taxgroup_map.put( "AMPQE", "porifera" ); + _default_taxcode_taxgroup_map.put( "AMPQU", "porifera" ); //TODO + _default_taxcode_taxgroup_map.put( "MONBE", "choanoflagellida" ); _default_taxcode_taxgroup_map.put( "SALS5", "choanoflagellida" ); _default_taxcode_taxgroup_map.put( "AMOPA", "ichthyophonida & filasterea" ); _default_taxcode_taxgroup_map.put( "SARXX", "ichthyophonida & filasterea" ); + _default_taxcode_taxgroup_map.put( "SPHAR", "ichthyophonida & filasterea" ); //TODO + _default_taxcode_taxgroup_map.put( "CAPO3", "ichthyophonida & filasterea" ); + _default_taxcode_taxgroup_map.put( "CAPOW", "ichthyophonida & filasterea" ); //TODO + _default_taxcode_taxgroup_map.put( "AALXX", "dikarya" ); _default_taxcode_taxgroup_map.put( "GIBZE", "dikarya" ); _default_taxcode_taxgroup_map.put( "HYPVG", "dikarya" ); @@ -197,6 +207,8 @@ final class TaxonomyUtil { _default_taxcode_taxgroup_map.put( "AGABU", "dikarya" ); _default_taxcode_taxgroup_map.put( "COPC7", "dikarya" ); _default_taxcode_taxgroup_map.put( "LACBS", "dikarya" ); + _default_taxcode_taxgroup_map.put( "LACBI", "dikarya" ); //TODO + _default_taxcode_taxgroup_map.put( "PLEOS", "dikarya" ); _default_taxcode_taxgroup_map.put( "CPUXX", "dikarya" ); _default_taxcode_taxgroup_map.put( "SERL9", "dikarya" ); @@ -336,8 +348,13 @@ final class TaxonomyUtil { _default_taxcode_taxgroup_map.put( "BODSA", "excavata" ); _default_taxcode_taxgroup_map.put( "NAEGR", "excavata" ); _default_taxcode_taxgroup_map.put( "GIAIC", "excavata" ); + _default_taxcode_taxgroup_map.put( "GIALA", "excavata" ); //TODO + _default_taxcode_taxgroup_map.put( "TRIVA", "excavata" ); _default_taxcode_taxgroup_map.put( "TTRXX", "apusozoa" ); + _default_taxcode_taxgroup_map.put( "THETR", "apusozoa" ); //TODO //FIXME + + _default_taxcode_taxgroup_map.put( "METAC", "archaea" ); _default_taxcode_taxgroup_map.put( "METBF", "archaea" ); _default_taxcode_taxgroup_map.put( "METMA", "archaea" ); -- 1.7.10.2